I think this is more of a 2 shop deal Justin.
First pull the drake, then have the hull re-glassed so there are no holes. Second, call your pump guy of choice to have him set your new berk intake and cut the hole for the bowl.
To have a intake set runs around $400-500, and I couldn't begin to tell you how much it would cost to re-glass the hull. For that call Sal at Orange County boat repair in Stanton CA (714) 827-6247. Or for that matter, see how much John at Ultra would get to have one of his guys do the repair.
Chris